Method-specific scCODA wrapper used by RunProportionTest. Calls Python helper via reticulate and falls back to sample-level summaries when unavailable.
Usage
RunProportionTestScCODA(
srt,
group.by,
split.by,
sample.by,
comparison = NULL,
reference_cell_type = NULL,
credible_effect_threshold = 0.95,
n_mcmc_samples = 20000L,
n_bootstrap = 500,
seed = 11,
verbose = TRUE
)Arguments
- srt
A Seurat object.
- group.by
Cell-type metadata column.
- split.by
Condition metadata column.
- sample.by
Sample metadata column.
- comparison
Optional comparisons to perform.
- reference_cell_type
Optional scCODA reference cell type.
- credible_effect_threshold
Inclusion probability threshold for credible effects.
- n_mcmc_samples
Requested MCMC sample count.
- n_bootstrap
Fallback bootstrap iterations.
- seed
Random seed.
- verbose
Whether to print messages.